rs1515024

Positions:

• chrX-79559798-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.109 in 111,216 control chromosomes in the GnomAD database, including 625 homozygotes. There are 3,761 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.11 (625 hom., 3761 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.109 AC: 12068 AN: 111162 Hom.: 623 Cov.: 23 AF XY: 0.112 AC XY: 3755 AN XY: 33586

Gnomad AFR AF: 0.0210

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.0827

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.0214

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.134

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.103

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.109 AC: 12075 AN: 111216 Hom.: 625 Cov.: 23 AF XY: 0.112 AC XY: 3761 AN XY: 33650

Gnomad4 AFR AF: 0.0209

Gnomad4 AMR AF: 0.0826

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.0215

Gnomad4 SAS AF: 0.363

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.144

Gnomad4 OTH AF: 0.105

Alfa AF: 0.146 Hom.: 6613

Bravo AF: 0.0948

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.055
DANN	Benign	0.53

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1515024; hg19: chrX-78815295;